>Does anyone know at which point during the boot sequence, BSD begins using
>its own disk I/O drivers and stops using the BIOS.  

After the kernel is loaded - ie, when you start seeing lines like:
NetBSD 1.1B (EXCALIBUR) #14: Wed Mar 27 00:15:10 EST 1996

>I suspect that at the point of this switch over, the geometry
>information you have entered may no longer be recognized as valid.
>Perhaps your secondary controller BIOS was copied into RAM and this has
>been overwritten (or ignored) when the BSD boot started up.

When I had something like this similar happen to me, I needed to adjust the
geometry of the disk using pfdisk/fdiks, or something similar.  If you
think you have this problem, one test of this is to boot from a floppy,
but at the boot prompt, say "hd(0,a)/netbsd" instead of hitting return.

--Ken